easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data

• DOI: 10.1093/bioinformatics/bti571
• Publication Date: 2005-07-13T12:09:41Z
• Authors: K. Hoffmann; T. H. Lindner
• Keywords: Centimorgan; Linkage (software); Mendelian inheritance; SNP; Genetic linkage; Spurious relationship

Summary: We extended the original easyLINKAGE program by enabling linkage analyses for large-scale SNP data in addition to those of microsatellites. implemented new modules Allegro, Merlin, SimWalk, GeneHunter Imprinting, TwoLocus, SuperLink and FastSLink automatic loop breaking outputs. added conditional as well multipoint simulation studies, error test routines checking Mendelian/non-Mendelian genotyping errors deviations from Hardy–Weinberg equilibrium. Data can be analyzed sets markers, defined centimorgan intervals using different allele frequency algorithms. The outputs consist genome-wide chromosomal postscript plots LOD scores, NPL P-values other parameters.